From comparative analyses of the nucleotide sequences of genes encoding ribosomal RNAs and several proteins, molecular phylogeneticists have constructed a “universal tree of life,” taking it as the basis for a “natural” hierarchical classification of all living things. Although confidence in some of the tree's early branches has recently been shaken, new approaches could still resolve many methodological uncertainties.More challenging is evidence that most archaeal and bacterial genomes (and the inferred ancestral eukaryotic nuclear genome) contain genes from multiple sources. If “chimerism” or “lateral gene transfer” cannot be dismissed as trivial in extent or limited to special categories of genes, then no hierarchical universal classification can be taken as natural. Molecular phylogeneticists will have failed to find the “true tree,” not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree. However, taxonomies based on molecular sequences will remain indispensable, and understanding of the evolutionary process will ultimately be enriched, not impoverished.

1 Center for Demographic and Population Genetics, The University of Texas at Houston, Houston, Texas 77025

With the aim of analyzing and interpreting data on DNA polymorphism obtained by DNA sequencing or restriction enzyme technique, a mathematical theory on the expected evolutionary relationship among DNA sequences (nucleons) sampled is developed under the assumption that the evolutionary change of nucleons is determined solely by mutation and random genetic drift. The statistical property of the number of nucleotide differences between randomly chosen nucleons and that of heterozygosity or nucleon diversity is investigated using this theory. These studies indicate that the estimates of the average number of nucleotide differences and nucleon diversity have a large variance, and a large part of this variance is due to stochastic factors. Therefore, increasing sample size does not help reduce the variance significantly. The distribution of sample allele (nucleomorph) frequencies is also studied, and it is shown that a small number of samples are sufficient in order to know the distribution pattern.

Edited* by David L. Dilcher, Indiana University, Bloomington, IN, and approved January 24, 2012 (received for review September 13, 2011)

Abstract

Plant communities of the geologic past can be reconstructed with high fidelity only if they were preserved in place in an instant in time. Here we report such a flora from an early Permian (ca. 298 Ma) ash-fall tuff in Inner Mongolia, a time interval and area where such information is filling a large gap of knowledge. About 1,000 m2 of forest growing on peat could be reconstructed based on the actual location of individual plants. Tree ferns formed a lower canopy and either Cordaites, a coniferophyte, or Sigillaria, a lycopsid, were present as taller trees. Noeggerathiales, an enigmatic and extinct spore-bearing plant group of small trees, is represented by three species that have been found as nearly complete specimens and are presented in reconstructions in their plant community. Landscape heterogenity is apparent, including one site where Noeggerathiales are dominant. This peat-forming flora is also taxonomically distinct from those growing on clastic soils in the same area and during the same time interval. This Permian flora demonstrates both similarities and differences to floras of the same age in Europe and North America and confirms the distinct character of the Cathaysian floral realm. Therefore, this flora will serve as a baseline for the study of other fossil floras in East Asia and the early Permian globally that will be needed for a better understanding of paleoclimate evolution through time.

“Most importantly, the campaign of the scientific establishment to rule out intelligent design as beyond discussion because it is not science results in the avoidance of significant questions about the relation between evolutionary theory and religious belief, questions that must be faced in order to understand the theory and evaluate the scientific evidence for it.” — Thomas Nagel, prominent philosopher of science and atheist.

Received 20 July 2011 Accepted 17 January 2012 Published 21 February 2012

Abstract

During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3 paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit.

Received 26 October 2011 Accepted 19 January 2012 Published 21 February 2012

Abstract

Rotary ATPases couple ATP hydrolysis/synthesis with proton translocation across biological membranes and so are central components of the biological energy conversion machinery. Their peripheral stalks are essential components that counteract torque generated by rotation of the central stalk during ATP synthesis or hydrolysis. Here we present a 2.25-Å resolution crystal structure of the peripheral stalk from Thermus thermophilus A-type ATPase/synthase. We identify bending and twisting motions inherent within the structure that accommodate and complement a radial wobbling of the ATPase headgroup as it progresses through its catalytic cycles, while still retaining azimuthal stiffness necessary to counteract rotation of the central stalk. The conformational freedom of the peripheral stalk is dictated by its unusual right-handed coiled-coil architecture, which is in principle conserved across all rotary ATPases. In context of the intact enzyme, the dynamics of the peripheral stalks provides a potential mechanism for cooperativity between distant parts of rotary ATPases.

There are numerous ways to display a phylogenetic tree, which is reflected in the diversity of software tools available to phylogenetists. Displaying very large trees continues to be a challenge, made ever harder as increasing computing power enables researchers to construct ever-larger trees. At the same time, computing technology is enabling novel visualisations, ranging from geophylogenies embedded on digital globes to touch-screen interfaces that enable greater interaction with evolutionary trees. In this review, I survey recent developments in phylogenetic visualisation, highlighting successful (and less successful) approaches and sketching some future directions.

Taxonomists are arguably the most active annotators of the natural world, collecting and publishing millions of phenotype data annually through descriptions of new taxa. By formalizing these data, preferably as they are collected, taxonomists stand to contribute a data set with research potential that rivals or even surpasses genomics. Over a decade of electronic innovation and debate has initiated a revolution in the way that the biodiversity is described. Here, we opine that a new generation of semantically based digital scaffolding, presently in various stages of completeness, and a commitment by taxonomists and their colleagues to undertake this transformation, are required to complete the taxonomic revolution and critically broaden the relevance of its products.

The accelerating growth of data and knowledge in evolutionary biology is indisputable. Despite this rapid progress, information remains scattered, poorly documented and in formats that impede discovery and integration. A grand challenge is the creation of a linked system of all evolutionary data, information and knowledge organized around Darwin's ever-growing Tree of Life. Such a system, accommodating topological disagreement where necessary, would consolidate taxon names, phenotypic and geographical distributional data across clades, and serve as an integrated community resource. The field of evolutionary informatics, reviewed here for the first time, has matured into a robust discipline that is developing the conceptual, infrastructure and community frameworks for meeting this grand challenge.

domingo, fevereiro 19, 2012

James A. Shapiro, Author, 'Evolution: A View from the 21st Century;' Professor of Microbiology, University of Chicago

What Is the Key to a Realistic Theory of Evolution?

Posted: 02/16/2012 5:55 pm

In The Origin of Species by Means of Natural Selection, Charles Darwin proposed to explain how one life form gave rise to another. He subtitled the book, "The Preservation of Favoured Races in the Struggle for Life." He argued that a succession of small improvements in reproductive success would gradually lead to the major changes that distinguish one species from another. This gradualist hypothesis followed the Uniformitarian principle learned from his geology professor, Charles Lyell.

Since 1859, Darwin's followers have focused on optimizing reproductive success, now called "fitness." For them, natural selection increases fitness and, thus, generates new life forms, including their sophisticated and complex adaptations.

Darwin put it this way in Chapter 6: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case."

There has always been controversy about whether random variation and natural selection for improved fitness can truly explain biological evolution over time. Today we can apply genome sequence data to test Darwin's theory. It answers clearly about gradualism.

Many genome changes at key stages of evolution have been neither small nor gradual. For example, plant breeders are familiar with rapid speciation. When we wish to create new plant species artificially, we do not use selection. We generate hybrids by mating different species. In a fine 1951 (!) Scientific American article on this subject entitled "Cataclysmic Evolution," the distinguished 20th Century evolutionist, G. Ledyard Stebbins, explained how flour wheat evolved, suddenly, by hybridization.

Hybridization frequently leads to a process of "whole genome doubling." Doubling the genome takes one generation and potentially affects all hereditary traits. Note that the production of new species with novel characters by hybridization occurs too rapidly for natural selection to act creatively.

Perhaps the most important evolutionary step of all took place at least one billion years ago, when two or more cells fused to produce the first "eukaryotic" cell having a defined nucleus. This nucleated cell was apparently the progenitor of all "higher" forms of life, including plants and animals. Such cell mergers are known as "symbiogenesis," long championed as an evolutionary force by the recently deceased biologist, Lynn Margulis .

It's remarkable that even though processes like hybridization and symbiogenesis have been well-known for decades, many neo-Darwinists firmly insist on gradualism in evolutionary change. Their position notwithstanding, living organisms have many tools at their disposal for generating sudden change.

As I described in my previous HuffPost blog, "Evolutionary Lessons from Superbugs," bacteria get new DNA information from unrelated organisms. Microbes transform into superbugs in a few minutes by "horizontal DNA transfer." Similar events confer new traits to many microbial and eukaryotic recipients, often multiple characters in a single step.

Was Darwin simply mistaken about the gradual nature of hereditary variation? Such ignorance would be unavoidable before we knew about Mendelian genetics and DNA. Or was there a deeper flaw in the theory that he (and Alfred Russell Wallace) propounded? The answer may well be that it was a basic mistake to think that optimizing fitness is the source of biological diversity.

The 2011 Nobel Prize in Chemistry was awarded to a materials scientist, Dan Shechtman, for the discovery of quasicrystals. The usual rumblings followed — why not include Paul Steinhardt, how about Roger Penrose? And, among chemists, a different tune, with an angry, resigned note to it, “Once again, not a real chemist …”

I want to address this attitude in this Editorial. First a few words about the Nobel Prizes.

I discuss the historical roots of the landscape problem and propose criteria for its successful resolution. This provides a perspective to evaluate the possibility to solve it in several of the speculative cosmological scenarios under study including eternal inflation, cosmological natural selection and cyclic cosmologies.

Invited contribution for a special issue of Foundations of Physics titled Forty Years Of String Theory: Reflecting On the Foundations.

THE rogue proteins behind variant CJD, the human form of mad cow disease, have revealed their benign side. Prions, it seems, lie at the heart of a newly discovered form of near-instant evolution that provides life with a third way to adapt to potentially lethal environments. Crucially, it involves neither genetic nor epigenetic changes to DNA.

The conventional view is that new traits can only evolve if DNA itself changes in some way. The classic way to do this is by mutating the genetic code itself. More recently, researchers have discovered that molecules can clamp onto DNA and prevent some parts of the sequence from being read, leading to genetic changes through a process that is known as epigenetics.

Yeast breaks the mould. In challenging conditions, it can instantly churn out hundreds of brand-new and potentially lifesaving proteins from its DNA, all without changing the genes in any way. Instead, yeast alters the way genes are read. The tiny fungi convert a special type of protein called Sup35 into a prion.

Sup35 normally plays an important role in the protein production line. It makes sure that the ribosomes within cells, in which the proteins are built, start and stop reading an RNA strand at just the right points to generate a certain protein.

When Sup35 transforms into a prion, it no longer performs that role. With this quality control missing, the entire gene sequence is read as it spools through the ribosome. This generates new proteins from sections of RNA that are usually ignored (see diagram).

The result is that the yeast generates a hotchpotch of brand-new proteins without changing its DNA in any way. Within that mix of new proteins could be some that are crucial for survival.

Susan Lindquist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, first saw this process, which she calls "combinatorial evolution", in 2004, while studying lab-grown Baker's yeast (Saccharomyces cerevisiae).

"We've been saying this is really cool and a way of producing new traits for years, but other people have said it's a disease of lab yeast," she says.

Now she's proved the sceptics wrong by demonstrating beyond doubt that the same process happens in nature too. She has seen it at work in 255 of 700 natural yeasts she and her colleagues have studied (Nature, DOI: 10.1038/nature10875).

Lindquist grew the yeast in a hostile environment - either oxygen-depleted or abnormally acidic, for example - and then exposed the survivors to a chemical that destroys prions. Many colonies withered, showing that the prions were responsible for their competitive edge.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the “hatcheries” of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K+, Zn2+, Mn2+, and phosphate. Thus, protocells must have evolved in habitats with a high K+/Na+ ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO2-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K+, Zn2+, and phosphorous compounds.

†“But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, light, heat, electricity &c. present, that a protein compound was chemically formed, ready to undergo still more complex changes….” —from Darwin's 1871 letter to Joseph Hooker (17).

‡ZnS, broadly known as phosphor (from “phosphorescence”), shows a unique ability to convert diverse kinds of energy, including that of light quanta, X-rays, electrons (as in displays), α-particles (ZnS was introduced as the first inorganic scintillator by Sir William Crookes in 1903), into (electro)chemical energy of separated electric charges (reviewed in ref. 10).